The chief executive of Universities UK, Nicola Dandridge, said they are "concerned about the methods used" in the making of the BBC Panorama programme, after an academic trip with LSE students was used to gain entry to North Korea.
Ms Dandridge said universities must be able to work with integrity and operate in sensitive areas of the world.
"The UK's academics have a global reputation, and it is vitally important that they can be trusted and seen to be working in an open and transparent manner", she said.
"The way that this BBC investigation was conducted might not only have put students' safety at risk, but may also have damaged our universities' reputations overseas", Ms Dandridge continued.
"We regret the BBC's approach in this matter. Universities UK will be seeking to discuss this with the BBC to ensure they fully understand the concerns of the university sector".
The head of the LSE student union has attacked the BBC accusing it of organising a student trip to North Korea "potentially as a ruse for them to get into North Korea".
Alex Peters-Day told BBC News: "We don't know what could have happened to those students [if it had been discovered that were accompanying BBC journalists] and crucially neither does the BBC".
She called on the BBC to pull the programme, which is due to air on Monday, and also demanded a full apology.